1. AP/IB Biology Chapter 2 The Chemistry of Life
Domains of Study
Domain of BioMolecules
Domain of Cells
Domain of Organisms
Domain of Populations
Domain of Communities

2. Why are we studying chemistry?
Chemistry is the foundation of biology.
Biology is really chemistry in that most biological processes are chemical reactions.

3. Everything is made of matter Matter is made of atoms
Hydrogen
1 proton
1 electron
Oxygen
8 protons
8 neutrons
8 electrons
Proton +
Neutron
Electron –

4. Different kinds of atoms =different elements
The World of Elements H C N O Na Mg P S K Ca
Different kinds of atoms =different elements

5. About 25 elements are essential for life
Four elements make up 96% of living matter:
• carbon (C) • hydrogen (H)
• oxygen (O) • nitrogen (N)
Five additional elements are important in living things:
• phosphorus (P) • calcium (Ca)
• sulfur (S) • iron (Fe)
sodium (Na)

6. Essential Elements of Life
Trace elements are those required by an organism in minute quantities.
Missing essential elements can greatly affect living organisms.
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7. Figure 2.4 The effects of essential-element deficiencies
Fig. 2-4a
Figure 2.4 The effects of essential-element deficiencies
(a) Nitrogen deficiency

8. Figure 2.4 The effects of essential-element deficiencies
Fig. 2-4b
Figure 2.4 The effects of essential-element deficiencies
(b) Iodine deficiency

9. Role of some elements in living things:
Sulfur
In plants – In some amino acids
In animals – In some amino acids
In prokaryotes – In some amino acids
Calcium
In plants – Cofactor in some enzymes
In animals – Cofactor in some enzymes and component of bones
In prokaryotes – Cofactor in some enzymes

10. Role of some elements in living things:
Phosphorous –
In plants – Phosphate groups in ATP
In animals – Phosphate groups in ATP
In prokaryotes – Phosphate groups in ATP
Iron –
In plants – In cytochromes
In animals – In cytochromes and in hemoglobin
In prokaryotes – In cytochromes

11. Role of some elements in living things:
Sodium –
In plants – In membrane function
In animals – In membrane function and sending nerve impulses
In prokaryotes – In membrane function

12. How does this atom behave?
Bonding properties
Effect of electrons
Electrons determine chemical behavior of an atom.
Depends on number of electrons in atom’s outermost shell
or energy level.
(Add this)Valence shell is another
name for outer shell.
How does this atom behave?

13. How does this atom behave? How does this atom behave?
Bonding properties
Effect of electrons
Atoms are stable when outer shell is full or has 8 electrons (Octet rule)
Sulfur on the LEFT
Magnesium on the RIGHT
How does this atom behave?
How does this atom behave?

14. Elements & their valence shells
Elements in the same row have the same number of en. levels.
Moving from left to right, each element has a sequential addition of electrons (& protons)

15. Elements & their valence shells
Elements in the same column have the same valence & similar chemical properties
Oxygen has medium electronegativity so doesn’t pull electrons all the way off hydrogen whereas chlorine would.
So oxygen forms a polar covalent bond.
Carbon has only a weak electronegativity so forms a nonpolar covalent bond

16. This tendency drives chemical reactions… and creates chemical bonds
Chemical reactivity
Atoms tend to
complete a partially filled valence shell or
empty a partially filled valence shell
This tendency drives chemical reactions…
and creates chemical bonds – –

17. Bonds in Biology Weak bonds Strong bonds Hydrogen bond hydrogen bonds
H2O
Weak bonds
hydrogen bonds
attraction between + and –
hydrophobic & hydrophilic interactions
van derWaals forces
ionic bonds (sometimes weak)
Strong bonds
covalent bonds- share electrons
ionic bonds - transfer electrons;
(sometimes strong)

18. Covalent Bonds
A covalent bond is the sharing of a pair of valence electrons by two atoms
In a covalent bond, the shared electrons count as part of each atom’s valence shell
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

19. Covalent bonds Why is this a strong bond? Forms molecules
Two atoms share a pair of electrons
Both atoms holding onto the electrons
Very stable
Forms molecules H
Oxygen – H O
H — H
H2 (hydrogen gas)
H2O (water)

20. A compound is a combination of two or more different elements
Covalent bonds can form between atoms of the same element or atoms of different elements
A compound is a combination of two or more different elements
Bonding capacity is called the atom’s valence
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

21. A molecule consists of two or more atoms held together by covalent bonds
A single covalent bond, or single bond, is the sharing of one pair of valence electrons
A double covalent bond, or double bond, is the sharing of two pairs of valence electrons
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

22. Multiple covalent bonds
2 atoms can share >1 pair of electrons
double bonds
2 pairs of electrons
triple bonds
3 pairs of electrons
Very strong bonds H
H–C–H –

23. Polar covalent bonds Pair of electrons shared unequally by 2 atoms
Water = O + H
Oxygen has stronger “attraction” for the electrons than hydrogen
Oxygen has higher electronegativity
Water is a polar molecule
“+” and “–” poles
Leads to many interesting properties of water… + – H
Oxygen – – – +

24. Electronegativity is an atom’s attraction for the electrons in a covalent bond
The more electronegative an atom, the more strongly it pulls shared electrons toward itself
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

25. In a nonpolar covalent bond, the atoms share the electron equally.
In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally
Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

26. Fig. 2-13
 – O H H + +
Figure 2.13 Polar covalent bonds in a water molecule
H2O

27. Hydrogen bonding Polar water creates molecular attractions Weak bond
Positive H atom in one H2O molecule is attracted to negative O in another H2O.
Also can occur wherever an -OH exists in a larger molecule.
Weak bond
Typical strength of 5.0
kcal/mol, but it varies.
APBio/TOPICS/Biochemistry/MoviesAP/03_02WaterStructure_A.swf
Weak bonds are still
important!

28. Oxygen – Significantly larger nucleus
Greater charge (+8)
Hydrogen – Smaller nucleus
Charge of (+1)
Electron pair found closer to the oxygen nucleus than the hydrogen nucleus.
Oxygen carries a small negative dipole,
and hydrogen carries a small positive dipole.

29. Molecular Shape and Function
A molecule’s shape is usually very important to its function
A molecule’s shape is determined by the positions of its atoms’ valence orbitals
In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes
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30. Hybridization of orbitals (a)
Fig. 2-17a
Four hybrid orbitals z
s orbital
Three p
orbitals x y
Tetrahedron
Figure 2.17 Molecular shapes due to hybrid orbitals
Hybridization of orbitals
(a)

31. Molecules with similar shapes can have similar biological effects
Biological molecules recognize and interact with each other with a specificity based on molecular shape
Molecules with similar shapes can have similar biological effects
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

32. Structures of endorphin and morphine
Fig. 2-18a
Key
Carbon
Nitrogen
Hydrogen
Sulfur
Natural endorphin
Oxygen
Morphine
Figure 2.18 A molecular mimic
(a)
Structures of endorphin and morphine

33. Binding to endorphin receptors
Fig. 2-18b
Natural
endorphin
Morphine
Endorphin
receptors
Brain cell
Figure 2.18 A molecular mimic
(b)
Binding to endorphin receptors

34. Concept 2.4: Chemical reactions make and break chemical bonds
Chemical reactions are the making and breaking of chemical bonds
The starting molecules of a chemical reaction are called reactants
The final molecules of a chemical reaction are called products
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings

35. Some chemical reactions go to completion: all reactants are converted to products
Many chemical reactions are reversible: products of the forward reaction become reactants for the reverse reaction
Chemical equilibrium is reached when the forward and reverse reaction rates are equal
Copyright © 2008 Pearson Education, Inc., publishing as Benjamin Cummings